代表论文：

1. Yizheng Wang, Yixiao Zhai, Yijie Ding*, Quan Zou*. SBSM-Pro: support bio-sequence machine for proteins. Science China Information Sciences. 2024, 67(11): 144-159. (web) 谷歌学术引用次
2. Jiacheng Wang, Yaojia Chen, Quan Zou*. Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model. PLoS Genetics. 2023, 19(9): e1010942 (codes)谷歌学术引用次
3. Furong Tang, Jiannan Chao, Yanming Wei, Fenglong Yang, Yixiao Zhai, Lei Xu, Quan Zou*. HAlign 3: fast multiple alignment of ultra-large numbers of similar DNA/RNA sequences. Molecular Biology and Evolution. 2022,39(8):msac166. (codes)谷歌学术引用次
4. Chao Wang*, Quan Zou*. MFPSP: identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm. PLoS Computational Biology. 2024, 20(11): e1012607. (codes)谷歌学术引用次
5. Tao Wang, Linlin Zhuo*, Yifan Chen, Xiangzheng Fu*, Xiangxiang Zeng, Quan Zou*. ECD-CDGI: an efficient energy-constrained diffusion model for cancer driver gene identification. PLoS Computational Biology. 2024, 20: e1012400谷歌学术引用次
6. Yixiao Zhai, Jiannan Chao, Yizheng Wang, Pinglu Zhang, Furong Tang, Quan Zou*. TPMA: a two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments. PLoS Computational Biology. 2024, 20(4): e1011988 (codes)谷歌学术引用次
7. Yaojia Chen, Jiacheng Wang, Chunyu Wang, Quan Zou*. AutoEdge-CCP: A Novel Approach for Predicting Cancer-Associated CircRNAs and Drugs based on Automated Edge Embedding. PLoS Computational Biology. 2024, 20(1): e1011851 (codes)谷歌学术引用次
8. Ran Su, Haitang Yang, Leyi Wei*, Siqi Chen*, Quan Zou*. A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data. PLoS Computational Biology. 2022, 18(9): e1010402 (codes)谷歌学术引用次
9. Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou*. A comprehensive overview and evaluation of circular RNA detection tools. PLoS Computational Biology. 2017,13(6): e1005420 (data and codes)(BibTeX, EndNote)谷歌学术引用次
10. Quan Zou*, Pengwei Xing, Leyi Wei, Bin Liu*. Gene2vec: Gene Subsequence Embedding for Prediction of Mammalian N6‐Methyladenosine Sites from mRNA. RNA. 2019, 25(2): 205-218 (web server)(BibTeX, EndNote)谷歌学术引用次
11. Chen Cao*, Mengting Shao, Chunman Zuo, Devin Kwok, Lin Liu, Yuli Ge, Zilong Zhang, Feifei Cui, Mingshuai Chen, Rui Fan, Yijie Ding, Hangjin Jiang, Guishen Wang*, Quan Zou*. RAVAR: a curated repository for rare variant-trait associations. Nucleic Acids Research. 2024, 52(D1): D990-D997. (web server)谷歌学术引用次
12. Chen Cao, Jianhua Wang, Devin Kwok, Zilong Zhang, Feifei Cui, Da Zhao, Mulin Jun Li, Quan Zou*. webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study. Nucleic Acids Research. 2022, 50(D1): D1123-D1130. (web site)谷歌学术引用次
13. Mengting Niu, Chunyu Wang, Zhanguo Zhang*, Quan Zou*. A computational model of circRNA-associated diseases based on a graph neural network: prediction and case studies for follow-up experimental validation. BMC Biology. 2024, 22:24. (codes)谷歌学术引用次
14. Chao Wang, Quan Zou*. Prediction of protein solubility based on sequence physicochemical patterns and distributed representation information with DeepSoluE. BMC Biology. 2023, 21:12. (web server)谷歌学术引用次
15. Zhonghao Ren, Xiangxiang Zeng, Yizhen Lao, Heping Zheng, Zhuhong You, Hongxin Xiang, Quan Zou*. A spatial hierarchical network learning framework for drug repositioning allowing interpretation from macro to micro scale. Communications Biology. 2024, 7: 1413 (codes)谷歌学术引用次
16. Ximei Luo, Quan Zou*. Identifying the “stripe” transcription factors and cooperative binding related to DNA methylation. Communications Biology. 2024, 7: 1265. (codes)谷歌学术引用次
17. Quan Zou*, Qingh Hu, Maozu Guo, Guohua Wang*. HAlign: Fast Multiple Similar DNA/RNA Sequence Alignment Based on the Centre Star Strategy. Bioinformatics. 2015,31(15): 2475-2481. (Software)(该软件被OMICTOOLS推荐)(BibTeX, EndNote)谷歌学术引用次
18. Wei Tang, Shixiang Wan, Zhen Yang, Andrew E. Teschendorff*, Quan Zou*. Tumor Origin Detection with Tissue-Specific miRNA and DNA methylation Markers. Bioinformatics. 2018, 34(3): 398-406. (web server) (BibTeX, EndNote)谷歌学术引用次
19. Cangzhi Jia*, Yun Zuo, Quan Zou*. O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique. Bioinformatics. 2018, 34(12): 2029-2036.(web server)(该软件被OMICTOOLS推荐)(BibTeX, EndNote)谷歌学术引用次
20. Xiangxiang Zeng, Li Liu, Linyuan Lu*, Quan Zou*. Prediction of potential disease-associated microRNAs using structural perturbation method. Bioinformatics. 2018, 34(14): 2425-2432.(codes)(BibTeX, EndNote)谷歌学术引用次
21. Wenying He, Cangzhi Jia*, Quan Zou*. 4mCPred: Machine Learning Methods for DNA N⁴-methylcytosine sites Prediction. Bioinformatics. 2019, 35(4): 593-601 (web server)(该软件被OMICTOOLS推荐)谷歌学术引用次
22. Leyi Wei, Shasha Luan, Luis Eijy Nagai, Ran Su*, Quan Zou*. Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species. Bioinformatics. 2019, 35(8): 1326-1333. (web server)谷歌学术引用次
23. Leyi Wei*, Chen Zhou, Ran Su*, Quan Zou*. PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning. Bioinformatics. 2019, 35(21):4272-4280. (web server)谷歌学术引用次
24. Xiangzheng Fu, Lijun Cai, Xiangxiang Zeng*, Quan Zou*. StackCPPred: A Stacking and Pairwise Energy Content based Prediction of Cell-Penetrating Peptides and Their Uptake Efficiency. Bioinformatics. 2020, 36(10):3028-3034. (code)谷歌学术引用次
25. Yu Zhang, Quan Zou*. PPTPP: A novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning. Bioinformatics. 2020, 36(13): 3982-3987 (codes and data)谷歌学术引用次
26. Zijie Shen, Quan Zou*. Basic polar and hydrophobic properties are the main characteristics that affect the binding of transcription factors to methylation sites. Bioinformatics. 2020,36(15):4263-4268 (Supplementary data) 谷歌学术引用次
27. Xiaoqing Ru, Xiucai Ye*, Tetsuya Sakurai, Quan Zou*. NerLTR-DTA: Drug-target binding affinity prediction based on neighbor relationship and learning to rank. Bioinformatics. 2022, 38(7): 1964-1971. (codes and datasets)谷歌学术引用次
28. Zilong Zhang, Feifei Cui, Wei Su, Lijun Dou, Anqi Xu, Chen Cao, Quan Zou*. webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration. Bioinformatics. 2022, 38(13):3488-3489. (web server)谷歌学术引用次
29. Yansu Wang, Ximei Luo, Quan Zou*. Effector-GAN: prediction of fungal effector proteins based on pretrained deep representation learning methods and generative adversarial networks. Bioinformatics. 2022, 38(14):3541-3548. (web server)谷歌学术引用次
30. Chao Cao, Chunyu Wang, Shuhong Yang, Quan Zou*. CircSI-SSL: circRNA-binding site identification based on self-supervised learning. Bioinformatics. 2024, 40(1): btae004. (codes)谷歌学术引用次
31. Pinglu Zhang, Huan Liu, Yanming Wei, Yixiao Zhai, Qinzhong Tian, Quan Zou*. FMAlign2: A novel fast multiple nucleotide sequence alignment method for ultralong datasets. Bioinformatics. 2024, 40(1): btae014(codes) 谷歌学术引用次
32. Zhecheng Zhou, Qingquan Liao, Jinhang Wei, Linlin Zhuo*, Xiaonan Wu*, Xiangzheng Fu*,Quan Zou*. Revisiting Drug-Protein Interaction Prediction: A Novel Global-Local Perspective. Bioinformatics. 2024, 40(5): btae271. (codes)谷歌学术引用次
33. Yushan Qiu, Lingfei Yang, Hao Jiang*, Quan Zou*. scTPC: a novel semi-supervised deep clustering model for scRNA-seq data. Bioinformatics. 2024, 40(5): btae293 (codes)谷歌学术引用次
34. Matee Ullah, Shahid Akbar, Ali Raza, Quan Zou*. DeepAVP-TPPred: identification of antiviral peptides using transformed image-based localized descriptors and binary tree growth algorithm. Bioinformatics. 2024, 40(5): btae305 (codes)谷歌学术引用次
35. Wei Song, Lewen Xu, Chenguang Han, Zhen Tian*, Quan Zou*. Drug-target interaction predictions with multi-view similarity network fusion strategy and deep interactive attention mechanism. Bioinformatics. 2024, 40(6): btae346. (codes)谷歌学术引用次
36. Xinqian Ma, Xiangzheng Fu, Tao Wang, Linlin Zhuo*, Quan Zou*. GraphADT: Empowering Interpretable Predictions of Acute Dermal Toxicity with Multi-View Graph Pooling and Structure Remapping. Bioinformatics. 2024, 40(7): btae438. (codes)谷歌学术引用次
37. Shida He, Xiucai Ye, Sakurai Tetsuya, Quan Zou*. MRMD3.0: A Python tool and webserver for dimensionality reduction and data visualization via an ensemble strategy. Journal of Molecular Biology. 2023, 435: 168116 (web site)谷歌学术引用次